Bacterial nitric oxide synthases and uses thereof

ABSTRACT

The present invention relates to isolated nucleic acid molecules encoding nitric oxide synthases. The isolated nucleic acid molecules and their encoded protein or polypeptides are useful in methods for attaching a nitrogen group to a target moiety of a compound and for synthesizing a nitrogen-modified compound in a transgenic host cell. The present invention also relates to expression systems and host cells containing the nucleic acids of the present invention, as well as a method of recombinantly producing the nitric oxide synthases of the present invention.

This application claims the benefit of U.S. Provisional Patent Application Ser. No. 60/475,111, filed Jun. 2, 2003.

The subject matter of this application was made with support from the United States Government under USDA Grant No. 99-35303-8084. The U.S. Government may have certain rights.

FIELD OF THE INVENTION

The present invention relates to isolated nucleic acid molecules encoding nitric oxide synthases, the encoded isolated nitric oxide synthases, and the uses of these isolated nucleic acids and nitric oxide synthases for catalyzing nitration and nitrosylation reactions.

BACKGROUND OF THE INVENTION

Nitric oxide synthases (“NOSs”) are highly regulated enzymes that synthesize the potent cytotoxin and signal molecule nitric oxide (NO) from L-arginine (L-arg) (Alderton et al., Biochem J. 357:593-615 (2001)). In mammals, NOSs are responsible for many functions that range from protection against pathogens and tumor cells to blood pressure regulation and nerve transmission. The production of NO in mammals is catalyzed solely by three highly regulated isozymes of NOS (Alderton et al., Biochem J. 357:593-615 (2001); Pfeiffer et al., Angew. Chem. Int. Ed. 38:1714-1731 (1999); and Stuehr, Biochim. Biophys. Acta 1411:217-230 (1999)). In particular, NOSs produce NO from oxidation of L-arginine to L-citrulline via the intermediate N-hydroxy-L-Arg (NHA) (Alderton et al., Biochem J. 357:593-615 (2001); Pfeiffer et al., Angew. Chem. Int. Ed. 38:1714-1731 (1999); and Stuehr, Biochim. Biophys. Acta 1411:217-230 (1999)). Mammalian NOSs are homodimers that contain an N-terminal heme oxygenase domain (NOS_(oxy)) and a C-terminal flavoprotein reductase domain (NOS_(red)). The oxygenase domain binds L-Arg, heme and the redox-active cofactor 6R-tetrahydrobiopterin (H₄B), whereas the reductase domain binds FAD, FMN and NADPH. A calmodulin (CaM) binding sequence links the oxygenase and the reductase domains and regulates reduction of NOS_(oxy) by NOS_(red) in those isoforms that respond to Ca²⁺.

Genome sequencing has revealed truncated NOS proteins in some Gram-positive bacteria, including Deinococcus radiodurans, Staphylococcus aureus, Bacillus subtilis, B. halodurans and B. anthracis. In general, bacterial NOSs are homologous to the mammalian NOS_(oxy) but lack an associated NOS_(red) and N-terminal regions that bind Zn²⁺, the dihydroxypropyl side chain of H₄B, and the adjacent subunit of the dimmer (Pant et al., Biochemistry 41:11071-11079 (2002) and Adak et al., J. Biol. Chem. 277:16167-16171 (2002)). Nevertheless, the D. radiodurans NOS (deiNOS) and B. subtilis NOS (bsNOS) are dimeric, have a heme liganded by cysteine thiol, bind substrate L-Arg, and produce nitrogen oxide species in a manner dependent on pterin (either with H₄B or with the related cofactor tetrahydrofolate (THF) (Adak et al., Proc. Natl. Acad. Sci. 99:107-12 (2002); Pant et al., Biochemistry 41:11071-11079 (2002); and Adak et al., J. Biol. Chem. 277:16167-16171 (2002)). The crystal structure of B. subtilis NOS, complexed with L-Arg, confirmed that bacterial NOS proteins are similar to mammalian NOSs and NO production has been demonstrated when a mammalian reductase domain is supplied (Adak et al., J. Biol. Chem. 277:16167-16171 (2002)). The redox mechanism by which the pterins H₄B and analog THF support NO synthesis in bacterial NOSs mirrors that of the mammalian enzymes (Adak et al., J. Biol. Chem. 277:16167-16171 (2002)). A reductase protein that supplies electrons for bacterial NOS catalysis has not yet been identified, although comparisons of bacterial and mammalian NOS structures suggest a common mode of interaction for such a redox partner (Adak et al., J. Biol. Chem. 277:16167-16171 (2002)).

Nitrated and nitrosylated natural products, although relatively rare, represent important herbicides, antibiotics, nematicides, fungicides, insecticides, and anti-cancer agents. Nitrated compounds are also key components of explosives, propellants. Despite the importance of nitration and nitrosylation processes for the chemical industry, conventional nitration reactions have drawbacks that include low specificity, low yields, difficult temperature control, difficult product workups, and the generation of waste acids (Pagoria et al., Thermochim. Acta 384:187-204 (2002); and Agrawal, Prog. Energy Combust. Sci. 24:1-30(1998)). For pyrotechnics, elevated reaction temperatures limit production of unstable products. Regarding pharmaceuticals, greater control of reaction selectivity is desired (Eaton et al., J. Med. Chem. 16:290-291(1973); and Hazra et al., Org. Prep. Proced. Int. 31:315-319 (1999)). Although nitrated and nitrosylated compounds have vast importance in the pharmaceutical and high-energy materials industries, the chemical processes responsible for the nitration and nitrosylation processes have liabilities in efficacy, cost, and environmental impact. Thus, there is a need for alternative enzymes and methods for conducting nitration/nitrosylation reactions.

The present invention is directed to overcoming these and other deficiencies in the art.

SUMMARY OF THE INVENTION

The present invention relates to an isolated nucleic acid molecule encoding a nitric oxide synthase. The isolated nucleic acid molecule can (i) include a nucleotide sequence of SEQ ID NO:1, SEQ ID NO:3, and/or SEQ ID _ NO:5; (ii) include a nucleotide sequence that hybridizes to SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5 under stringent conditions characterized by a hybridization medium comprising about 5×SSC at a temperature of about 55° C.; (iii) include a nucleotide sequence having greater than 95 percent homology to a nucleic acid according to SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5; (iv) include a nucleotide sequence that encodes a nitric oxide synthase protein having an amino acid sequence that is at least 85 percent similar to either SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:6 by basic BLAST using default parameters analysis; (v) encode a nitric oxide synthase comprising a protein or polypeptide having an amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, and/or SEQ ID NO:6; (vi) encode a nitric oxide synthase comprising a protein or polypeptide having an amino acid motif of SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, and/or combinations thereof; or (vii) encode a nitric oxide synthase protein or polypeptide having an amino acid sequence of SEQ ID NO:47. Expression vectors (e.g., expression systems) and host cells which include the nucleic acid molecules of the present invention are also disclosed. Isolated NOS proteins or polypeptides encoded by the isolated nucleic acid molecules of the present invention are also disclosed. The present invention also relates to a method of recombinantly producing in a host cell the nitric oxide synthases encoded by the nucleic acid molecules of the present invention.

The present invention also relates to a method of attaching a nitrogen group to a target moiety of a compound. This method involves providing a nitric oxide synthase and a compound having a target moiety. The nitric oxide synthase and the compound are combined in a reaction mixture under conditions effective to allow the nitric oxide synthase to catalyze a reaction whereby a nitrogen group contained in the reaction mixture is attached to the target moiety. The method thereby yields a nitrogen-modified compound. Suitable nitric oxide synthases for use in this method can include: (i) a protein or polypeptide having an amino acid sequence that is at least 85 percent similar to either SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:6 by basic BLAST using default parameters analysis; (ii) a protein or polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, and SEQ ID NO:6; (iii) a protein or polypeptide having an amino acid motif such as the motif of SEQ ID NO:7, the motif of SEQ ID NO:8, the motif of SEQ ID NO:9, the motif of SEQ ID NO:10, the motif of SEQ ID NO:11, the motif of SEQ ID NO:12, the motif of SEQ ID NO:13, the motif of SEQ ID NO:14, the motif of SEQ ID NO:15, the motif of SEQ ID NO:16, the motif of SEQ ID NO:17, the motif of SEQ ID NO:18, the motif of SEQ ID NO:19, the motif of SEQ ID NO:20, the motif of SEQ ID NO:21, the motif of SEQ ID NO:22, the motif of SEQ ID NO:23, the motif of SEQ ID NO:24, the motif of SEQ ID NO:25, the motif of SEQ ID NO:26, the motif of SEQ ID NO:27, the motif of SEQ ID NO:28, the motif of SEQ ID NO:29, the motif of SEQ ID NO:30, the motif of SEQ ID NO:31, the motif of SEQ ID NO:32, the motif of SEQ ID NO:33, the motif of SEQ ID NO:34, the motif of SEQ ID NO:35, the motif of SEQ ID NO:36, the motif of SEQ ID NO:37, the motif of SEQ ID NO:38, the motif of SEQ ID NO:39, the motif of SEQ ID NO:40, the motif of SEQ ID NO:41, the motif of SEQ ID NO:42, the motif of SEQ ID NO:43, the motif of SEQ ID NO:44, the motif of SEQ ID NO:45, the motif of SEQ ID NO:46, and/or combinations thereof; or (iv) a protein or polypeptide having an amino acid sequence of SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, or SEQ ID NO:50.

The present invention further relates to a method of synthesizing a nitrogen-modified compound in a transgenic host cell. This method involves providing a transgenic host cell transformed with a DNA molecule encoding a nitric oxide synthase. This method also involves providing a non-modified compound containing a target moiety. The transgenic host cell and the non-modified compound are cultured in a culture medium under conditions effective to allow the nitric oxide synthase to be expressed and to catalyze a reaction whereby a nitrogen group contained in the host cell or in a culture medium attaches to the target moiety. The method thereby yields a nitrogen-modified compound. Suitable DNA molecules for use in this method can include those that: (i) have a nucleotide sequence of SEQ ID NO:1, SEQ ID NO:3, and SEQ ID NO:5; (ii) have a nucleotide sequence that hybridizes to SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5 under stringent conditions characterized by a hybridization medium comprising about 5×SSC at a temperature of about 55° C.; (iii) have a nucleotide sequence having greater than 95 percent homology to a nucleic acid according to SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5; (iv) have a nucleotide sequence that encodes a nitric oxide synthase protein having an amino acid sequence that is at least 85 percent similar to either SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:6 by basic BLAST using default parameters analysis; (v) encode a nitric oxide synthase having a protein or polypeptide having an amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, and SEQ ID NO:6; (vi) encode a nitric oxide synthase having a protein or polypeptide having amino acid motifs such as the motif of SEQ ID NO:7, the motif of SEQ ID NO:8, the motif of SEQ ID NO:9, the motif of SEQ ID NO:10, the motif of SEQ ID NO:11, the motif of SEQ ID NO:12, the motif of SEQ ID NO:13, the motif of SEQ ID NO:14, the motif of SEQ ID NO:15, the motif of SEQ ID NO:16, the motif of SEQ ID NO:17, the motif of SEQ ID NO:18, the motif of SEQ ID NO:19, the motif of SEQ ID NO:20, the motif of SEQ ID NO:21, the motif of SEQ ID NO:22, the motif of SEQ ID NO:23, the motif of SEQ ID NO:24, the motif of SEQ ID NO:25, the motif of SEQ ID NO:26, the motif of SEQ ID NO:27, the motif of SEQ ID NO:28, the motif of SEQ ID NO:29, the motif of SEQ ID NO:30, the motif of SEQ ID NO:31, the motif of SEQ ID NO:32, the motif of SEQ ID NO:33, the motif of SEQ ID NO:34, the motif of SEQ ID NO:35, the motif of SEQ ID NO:36, the motif of SEQ ID NO:37, the motif of SEQ ID NO:38, the motif of SEQ ID NO:39, the motif of SEQ ID NO:40, the motif of SEQ ID NO:41, the motif of SEQ ID NO:42, the motif of SEQ ID NO:43, the motif of SEQ ID NO:44, the motif of SEQ ID NO:45, the motif of SEQ ID NO:46, and/or combinations thereof; or (vii) encode a nitric oxide synthase having a protein or polypeptide having an amino acid sequence of SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, or SEQ ID NO:50.

The nitric oxide synthases of the present invention are useful for catalyzing specific nitration and/or nitrosylation reactions that can be used in developing more efficient and safe methods of producing nitrated and/or nitrosylated compounds. The present invention could also be useful for bioengineering new bioactive products by incorporation of nitration and nitrosylation events into existing biosynthetic pathways. The nitric oxide synthases of the present invention can also be used to broaden substrate specificity and fine-tune selectivity for the introduction of nitroso and nitro functionalities.

An additional advantage of enzymatically controlled nitration (as provided by the present invention) is the potential for discovering entirely new compounds through bioengineering. For example, genetic incorporation of bacterial NOS into polyketide or non-ribosomal peptide biosynthetic pathways (Kleinkauf et al., European Journal of Biochemistry 236:335-351 (1996); and Watanabe et al., J. BioL Chem. 278:42020-42026 (2003), which are hereby incorporated by reference in their entirety) will allow generation of novel natural products. Screened with suitable bioassays, nitrated compounds could produce novel leads for drug design.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1B show the chemical structure of thaxtomin A (FIG. 1A) and the genetic organization of the nos region in the thaxtomin-producing species Streptomyces turgidiscabies (FIG. 1B). Thaxtomin A is the predominant thaxtomin congener produced by plant pathogenic Streptomyces spp. As shown in FIG. 1B, the txtAB genes of Streptomyces turgidiscabies encode two similar peptide synthetases required for synthesis of the dipeptide (Healy et al., Mol. Micro. 38:794-804 (2000), which is hereby incorporated by reference in its entirety). The txtC gene encodes a P450 monooxygenase that is required for post-cyclization hydroxylation of the dipeptide. The nos gene is upstream of characterized thaxtomin biosynthetic genes.

FIG. 2 shows the amino acid sequence alignment of NOSs from Streptomyces turgidiscabies (stNOS), Bacillus subtilis (bsNOS), and murine iNOS (miNOS). FIG. 2 demonstrates that stNOS is homologous to NOS proteins from Bacillus subtilis (bsNOS) and the oxygenase domain of murine iNOS (miNOS). Residues involved in binding substrate L-Arg (bolded letters), pterin cofactor (underlined letters), heme iron and zinc cations (grey letters) are nearly completely conserved among these three classes of NOS_(oxy) proteins. Unlike other bacterial NOSs, stNOS contains an N-terminal extension involved in zinc ion and pterin side-chain binding in miNOS (secondary structure elements and structural motifs for bsNOS shown above in grey, see Pant et al., Biochemistry 41:11071 -11079 (2002), which is hereby incorporated by reference in its entirety, for nomenclature). The most C-terminal pterin binding residues (stNOS 385 and 386) vary among the proteins because interactions of these residues with pterin are main-chain mediated. Boxed residues indicate positions of different residue character between mammalian and bacterial NOSs. These changes primarily map to the pterin binding site and a site likely involved in reductase protein interactions. The change from Val to Ile at stNOS residue 259 is conserved in all bacterial proteins and increases protection of the immediate distal heme pocket compared to the mammalian proteins.

FIGS. 3A-3C show that deletion of nos reduces thaxtomin production by S. turgidiscabies. FIG. 3A shows a model for nos replacement in Streptomyces turgidiscabies car8 by the p2XNOS targeting vector using marker-exchange mutagenesis. FIG. 3B shows Southern hybridization of an internal 673 bp ^(α32)P labeled nos probe (left) or the ^(α32)P labeled 4.7 kb HindIII/EcoRI p2XNOS insert (right) to EcoRI digests of S. turgidiscabies wild-type (lane 1), Δnos (lane 2) Δnos pIJ8600 (empty vector) (lane 3), Δnos pIJ8600NOS (complemented vector)(lane 4) genomic DNA. The thiostrepton resistance gene (tsr) in the p2XNOS insert probe also hybridizes to tsr on pIJ8600 (lanes 3, 4). FIG. 3C shows confirmation of nos expression using RT-PCR. Dnase treated RNA, odd-numbered lanes, cDNA, even-numbered lanes. Wild-type S. turgidiscabies, lanes 1, 2; Δnos, lanes 3, 4; Δnos pIJ8600, lanes 5, 6; Δnos pIJ8600NOS, lanes 7, 8.

FIGS. 4A-4C shows that nitrite formation from N^(ω)-hydroxy-L-arginine by recombinant stNOS and sensitivity to inhibitors of mammalian NOSs. FIG. 4A shows Streptomyces turgidiscabies NOS Δ41 (residues 41-to carboxy-terminus) cloned into pet28 (Novagene) and expressed in E. coli BL-21 cells (lane 3). Full-length stNOS was rapidly degraded in E. coli, but the Δ41 construct, which contains all NOS homology regions, produced high levels of protein that were comparable to levels of recombinant Deinococcus radiodurans NOS¹⁰ (lane 2) and significantly above levels of background proteins expressed from cells containing the pet28 vector with no NOS insert (lane 1). Sonicated cell lysates from 3 mL cultures were run on 12% SDS-PAGE gels after 2.5 hr induction with 0.1 mM IPTG. Arrow shows the positions of recombinant deiNOS, and stNOS in lanes 2 and 3. FIG. 4B shows nitrite production by cell lysates depicted in FIG. 4A measured by the Griess assay. The NOS intermediate N^(ω)-hydroxy-L-arginine (2 mM) and hydrogen peroxide (4 mM) were reacted with 20 μL of cell lysates shown in FIG. 4A and assayed for nitrite with the Griess reagents after 15 min. Lysates from cells overexpressing stNOS generate nitrite at levels comparable to that of overexpressed deiNOS and significantly above that of the empty vector control (pet28). The selective mammalian NOS inhibitor, nitro-L-arginine (active form of nitro-L-arginine methyl ester), inhibits nitrite formation by lysates expressing stNOS when added to a concentration of 1 mM (same reaction conditions as above). FIG. 4C shows the L-arginine based NOS inhibitors nitro-L-arginine methyl ester (NAME) (32 μM), aminoguanidine (AG) (270 μM), NG-monomethyl-L-arginine (NMMA) (510 μM), and 7-nitroindazole (7-IN) (1.2 μM) each inhibit toxin product without affecting bacterial growth (Standard error reported, n=6).

FIGS. 5A-5B shows that the nitrate nitrogen derives from the guanidine nitrogen of L-Arg. Nuclear magnetic resonance analysis of thaxtomin A extracted from cultures fed either (FIG. 5A) L-Arginine-guanido-¹⁵N₂.HCl (Cambridge Isotope Laboratories), or (FIG. 5B) ¹⁵NH₄NO₃ (Aldrich). Based on literature values for ¹⁵N atoms in electronic environments similar to those of the four nitrogen atoms in thaxtomin A (Patel et al., Biochemica. Biophys. Acta. 1411:385-400 (1999), which is hereby incorporated by reference in its entirety), the two most upfield peaks at 125 and 114.6 ppm can be assigned to the N-methyls, the broad peak at 132.3 ppm can be assigned to the indole nitrogen, and the downfield peak at 374.8 ppm is diagnostic for the NO₂-nitrogen. Accordingly, the single peak (see FIG. 5A) in the spectrum of the L-Arg-guanidino-¹⁵N₂.HCl supplied sample, at 375.0 ppm represents the signal of the NO₂-nitrogen alone.

FIGS. 6A-6B show alignments of the amino acid sequences of the nitric oxide synthases from the following organisms (with the ATCC Accession Numbers representing the GenBank for the nos sequences): Bacillus anthracis (ATCC Accession No. AAP29327); Bacillus cereus (ATCC Accession No. AAP12306); Bacillus subtilis (ATCC Accession No. CAB12592); Bacillus halodurans (ATCC Accession No. BAB04542); Staphylococcus aureus (ATCC Accession No. BAB95720); Staphylococcus epidermidis (ATCC Accession No. AE016749); Deinococcus radiodurans (ATCC Accession No. AE002088); Mus musculus (ATCC Accession No. AAC52356); Streptomyces acidiscabies (ATCC Accession No. AY204508); Streptomyces scabies (ATCC Accession No. AY204507); Streptomyces turgidiscabies (ATCC Accession No. AY204509); and Streptomyces avermitilis (ATCC Accession No. BAC69241).

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to isolated nucleic acid molecules encoding nitric oxide synthases (“NOSs”). The nitric oxide synthases of the present invention share a common function, in that they function as catalysts for nitration and/or nitrosylation reactions. Also disclosed are expression systems and host cells containing such nucleic acid molecules, as well as isolated proteins or polypeptides encoded by the nucleic acid molecules. Uses of the nucleic acid molecules and the proteins or polypeptides encoded by the nucleic acid molecules are disclosed.

The isolated nucleic acid molecules and their encoded proteins or polypeptides can be, without limitation, from various Streptomyces species. Suitable Streptomyces species include, for example, Streptomyces acidiscabies, Streptomyces scabies, Streptomyces turgidiscabies, Streptomyces avermitilis, and Streptomyces ipomoea.

A first isolated nucleic acid molecule of the present invention encodes a nitric oxide synthase (“NOS”) from Streptomyces acidiscabies (see GenBank Accession No. AY204508) and has a nucleotide sequence according to SEQ ID NO:1 as follows: gtgacctccgaagtcgctctgggcccttccttgcccgccccgtccccgacagcgtgcccggcactg gggcccgattcgtcccttggcccggtcccgtcggcggaaccggcgacgccgcagtcctgcggcgtc gccgatccaaatgaggctgaggagttcctgcgccagttccacgcggagcagtccgatcagcccgtc ccgctcgcccggcgcctggagcaggtccgcgccgccatcgacgccacgggcacctaccggcacacc accgccgagctcgtgtacggtgcccgcgtcgcgtggcgcaactccagtcgctgcatcggccgcctg tactggaacagcctgcgcgtcctggaccgccgggacgccacagcccccgatgagatccaccggcac ttgtgcacgcacctgcgccaggcgaccaacggcgggcgcatcaggccggtgatttcggtcttcgcc ccggactcccccggccggcccggcccgcaggtgtggaacgagcagctcatccggtacgccggctac cgccgcgacgacggcaccgtgctcggtgacccgcgcaccgccgacctcaccgaggccatcctccgc ctcggctggcagggctgcccccaagggccgttcgacgtcctgcccctggtcatcgacacccccgac gacaaaccccggttcttcgagctgccgcgggagctggtcttggaggtccctatcacccaccccgac gtcccacgcctggccgaactgggcctgcgctggcacgccgtacccgtcatctccaacatgcgccta cgcatcggcgggatggactacccgctcgccccgttcaacggctggtacatgggcacggagatcggc gcccgcaacctcgtcgacgaggaccgctacaacatgctccccgccgtcgccgcctgcctccagctg gacaccaccagcgagtcaaccctgtggcgcgaccgcgccctggtcgagctcaacgtcgccgtcctg cactccttcgaggccgcaggtgtccggatcagcgaccaccacgaggagtcccggcgcttcctcgcc cacctggccaaggaggaacgccagggccgcaccgtatccgcagactggagctggatcgtccccccg ctctccggcggcatcacccccgtgttccaccgttactacgacaacgtcgaccagcgccccaacttc tacccccaccagtga

The NOS protein or polypeptide encoded by this nucleic acid molecule has an amino acid sequence according to SEQ ID NO:2 as follows: MTSEVALGPSLPAPSPTACPALGPDSSLGPVPSAEPATPQSCGVADPNEAEEFLRQFHAEQSDQPV PLARRLEQVRAAIDATGTYRHTTAELVYGARVAWRNSSRCIGRLYWNSLRVLDRRDATAPDEIHRH LCTHLRQATNGGRIRPVISVFAPDSPGRPGPQVWNEQLIRYAGYRRDDGTVLGDPRTADLTEAILR LGWQGCPQGPFDVLPLVIDTPDDKPRFFELPRELVLEVPITHPDVPRLAELGLRWHAVPVISNMRL RIGGMDYPLAPFNGWYMGTEIGARNLVDEDRYNMLPAVAACLQLDTTSESTLWRDRALVELNVAVL HSFEAAGVRISDHHEESRRFLAHLAKEERQGRTVSADWSWIVPPLSGGITPVFHRYYDNVDQRPNF YPHQ

A second isolated nucleic acid molecule of the present invention encodes a NOS from Streptomyces scabies (see GenBank Accession No. AY204507) and has a nucleotide sequence according to SEQ ID NO:3 as follows: gtgacctccgaagtcgctctgggcccttccttgcccgccccgtccccgacagcgtgcccggcactg gggcccgattcgtcccttggcccggtcccgtcggcggaaccggcgacgccgcagtcctgcggcgtc gccgatccaaatgaggctgaggagttcctgcgccagttccacgcggagcagtccgatcagcccgtc ccgctcgcccggcgcctggagcaggtccgcgccgccatcgacgccacgggcacctaccggcacacc accgccgagctcgtgtacggtgcccgcgtcgcgtggcgcaactccagtcgctgcatcggccgcctg tactggaacagcctgcgcgtcctggaccgccgggacgccacagcccccgatgagatccaccggcac ttgtgcacgcacctgcgccaggcgaccaacggcgggcgcatcaggccggtgatttcggtcttcgcc ccggactcccccggccggcccggcccgcaggtgtggaacgagcagctcatccggtacgccggctac cgccgcgacgacggcaccgtgctcggtgacccgcgcaccgccgacctcaccgaggccatcctccgc ctcggctggcagggctgcccccaagggccgttcgacgtcctgcccctggtcatcgacacccccgac gacaaaccccggttcttcgagctgccgcgggagctggtcttggaggtccctatcacccaccccgac gtcccacgcctggccgaactgggcctgcgctggcacgccgtacccgtcatctccaacatgcgccta cgcatcggcgggatggactacccgctcgccccgttcaacggctggtacatgggcacggagatcggc gcccgcaacctcgtcgacgaggaccgctacaacatgctccccgccgtcgccgcctgcctccagytg gacaccaccagcgagtcaaccctgtggcgcgaccgcgccctggtcgagctcaacgtcgccgtcctg cactccttcgaggccgcaggtgtccggatcagcgaccaccacgaggagtcccggcgcttcctcgcc cacctggccaaggaggaacgccagggccgcaccgtatccgcagactggagctggatcgtccccccg ctctccggcggcatcacccccgtgttccaccgttactacgacaacgtcgaccagcgccccaacttc tacccccaccagtga

The NOS protein or polypeptide encoded by this nucleic acid molecule has an amino acid sequence according to SEQ ID NO:4 as follows: MTSEVALGPSLPAPSPTACPALGPDSSLGPVPSAEPATPQSCGVADPNEAEEFLRQFHAEQSDQPV PLARRLEQVRAAIDATGTYRHTTAELVYGARVAWRNSSRCIGRLYWNSLRVLDRRDATAPDEIHRH LCTHLRQATNGGRIRPVISVFAPDSPGRPGPQVWNEQLIRYAGYRRDDGTVLGDPRTADLTEATIR LGWQGCPQGPFDVLPLVIDTPDDKPRFFELPRELVLEVPITHPDVPRLAELGLRWHAVPVISNMRL RIGGMDYPLAPFNGWYMGTEIGARNLVDEDRYNMLPAVAACLQLDTTSESTLWRDRALVELNVAVL HSFEAAGVRISDHHEESRRFLAHLAKEERQGRTVSADWSWIVPPLSGGITPVFHRYYDNVDQRPNF YPHQ

A third isolated nucleic acid molecule of the present invention encodes a from Streptomyces turgidiscabies (see GenBank Accession No. AY204509) and has a nucleotide sequence according to SEQ ID NO:5 as follows: gtgactttcgaagtcgccctgggcccttccttgcccgccccgtccccgacagcgtgcccggcgctg gcgcacgattcgcccctcagtcccgtcccgtcggcggaaccggcgacgtcgcaggactgcggcgtc gccgatccagacgaggccgaggagttcctgcgccagtttcacgcggagcagtccgaccaggccgtc ccgctcactcggcgcctggaccaggttcgcgctgccatcgacgccacgggcacctaccgtcatacc accgccgagctcgtgttcggtgcccgtgtcgcgtggcgcaactccagtcgctgtatcggccgcctg tactggaacagcctgcgcgtcctggaccgccgggacaccacagcccccgaggtaatccaccggcac ctttgcacgcacctgcgccaggcgaccaacggtgggcgtatcaggccggtgatttcggtcttcgcc ccggacgcacccagccgacccggcccgcgggtgtggaacgagcaactcgtccggtacgccggccac cgtcgcgacgacggcaccgtactcggcgacccgcgatctgccgacctcaccgaggccatccgcggc ctcggatggcagggaggccgccaagggccgttcgacgtcctgcccctggtcatcgacgcccacgac gacaaaccgcggttcttcgagctgccgcgggaggttgtcctggaggtccctatcacccaccccgac gtcccacgactggccgaactctgcctgcgctggcacgccgtacccgttatctccaacatgcgcctg cgtatcggcggggtggactaccccctcgccccgttcaacggctggtacatgggcacggagatcggc gtccgtaacctcgtcgacgaggcccgctacaacctgctccccgccgtggccgcctgcctccagttg gacaccaccagcgagtccaccctgtggcgtgaccgcgctctggtcgaactcaacgttgccgtcttg cactctttcgcggccgcaggcgtccggatcagtgaccaccacgaggagtcccggcgcttcctcgcc cacctgaccaaggaggaacgccagggccgcaccgtacccgcggactggagctggatcgtccctccg ctttccagcggcatcacccccgtcttccaccgctactacgacaacgccgaccagcgccccaacttt taccctcatcagtga

The NOS protein or polypeptide encoded by this nucleic acid molecule has an amino acid sequence according to SEQ ID NO:6 as follows: MTFEVALGPSLPAPSPTACPALAHDSPLSPVPSAEPATSQDCGVADPDEAEEFLRQFHAEQSDQAV PLTRRLDQVRAAIDATGTYRHTTAELVFGARVAWRNSSRCIGRLYWNSLRVLDRRDTTAPEVIHRH LCTHLRQATNGGRIRPVISVFAPDAPSRPGPRVWNEQLVRYAGHRRDDGTVLGDPRSADLTEAIRG LGWQGGRQGPFDVLPLVIDAHDDKPRFFELPREVVLEVPITHPDVPRLAELCLRWHAVPVISNMRL RIGGVDYPLAPFNGWYMGTEIGVRNLVDEARYNLLPAVAACLQLDTTSESTLWRDRALVELNVAVL HSFAAAGVRISDHHEESRRFLAHLTKEERQGRTVPADWSWIVPPLSSGITPVFHRYYDNADQRPNF YPHQ

Fragments of the above-identified proteins or polypeptides as well as fragments of full length proteins can also be used according to the present invention.

Suitable fragments can be produced by several means. Subclones of the gene encoding a known protein can be produced using conventional molecular genetic manipulation for subcloning gene fragments, such as described by Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Springs Laboratory, Cold Springs Harbor, N.Y. (1989), and Ausubel et al. (ed.), Current Protocols in Molecular Biology, John Wiley & Sons (New York, N.Y.) (1999 and preceding editions), each of which is hereby incorporated by reference in its entirety. The subclones then are expressed in vitro or in vivo in bacterial cells to yield a smaller protein or polypeptide that can be tested for activity. Various other cloning protocols known in the art are suitable for use in the present invention, including, for example, those described for Streptomyces in Hopwood et al., Genetic manipulation of Streptomyces: A Laboratory Manual, Norwich: John Innes Foundation (1985) and Kieser et al., Practical Streptomyces Genetics Norwich: John Innes Foundation (2000), which are hereby incorporated by reference in their entirety.

In another approach, based on knowledge of the primary structure of the protein, fragments of the protein-coding gene may be synthesized using the PCR technique together with specific sets of primers chosen to represent particular portions of the protein. Erlich, H. A., et al., “Recent Advances in the Polymerase Chain Reaction,” Science 252:1643-51 (1991), which is hereby incorporated by reference. These can then be cloned into an appropriate vector for expression of a truncated protein or polypeptide from bacterial cells as described above.

As an alternative, fragments of a protein can be produced by digestion of a full-length protein with proteolytic enzymes like chymotrypsin or Staphylococcus proteinase A, or trypsin. Different proteolytic enzymes are likely to cleave different proteins at different sites based on the amino acid sequence of the particular protein. Some of the fragments that result from proteolysis may be active virulence proteins or polypeptides.

Chemical synthesis can also be used to make suitable fragments. Such a synthesis is carried out using known amino acid sequences for the polypeptide being produced. Alternatively, subjecting a full length protein to high temperatures and pressures will produce fragments. These fragments can then be separated by conventional procedures (e.g., chromatography, SDS-PAGE).

Another example of suitable fragments of the nucleic acids of the present invention are fragments of the genes which have been identified as conserved (“con”) regions of the proteins, or alternatively, those portions of nucleotide sequences that have been identified as variable (“var”) regions. Conserved regions in accordance with the present invention are further described infra. Sequences identified using DNAStar Mega alignment program as either variable or conserved in a gene can be amplified using standard PCR methods using forward and reverse primers designed to amplify the region of choice and which include a restriction enzyme sequence to allow ligation of the PCR product into a vector of choice. Combinations of amplified conserved and variable region sequences can be ligated into a single vector to create a “cassette” which contains a plurality of DNA molecules in one vector.

Also suitable as an isolated nucleic acid molecule according to the present invention is a nucleic molecule having a nucleotide sequence that encodes a NOS protein or polypeptide having an amino acid motif that is a conserved region of the NOS protein or polypeptide from Streptomyces acidiscabies, Streptomyces scabies, and Streptomyces turgidiscabies (as described in Table 1, below). TABLE 1 Conserved Regions of the NOS Proteins or Polypeptides From Streptomyces acidiscabies, Streptomyces scabies, and Streptomyces turgidiscabies Location¹ Motif  4-22 EVALGPSLPAPSPTACPAL (SEQ ID NO: 7) 30-38 PVPSAEPAT (SEQ ID NO: 8) 42-47 CGVADP (SEQ ID NO: 9) 49-64 EAEEFLRQFHAEQSDQ (SEQ ID NO: 10) 74-93 QVRAAIDATGTYRHTTAELV (SEQ ID NO: 11) 95-122 GARVAWRNSSRCIGRLYWNSLRVLDRRD (SEQ ID NO: 12) 129-156 IHRHLCTHLRQATNGGRIRPVISVFAPD (SEQ ID NO: 13) 165-170 VWNEQL (SEQ ID NO: 14) 177-188 RRDDGTVLGDPR (SEQ ID NO: 15) 190-196 ADLTEAI (SEQ ID NO: 16) 199-203 LGWQG (SEQ ID NO: 17) 206-217 QGPFDVLPLVID (SEQ ID NO: 18) 220-231 DDKPRFFELPRE (SEQ ID NO: 19) 233-249 VLEVPITHPDVPRLAEL (SEQ ID NO: 20) 251-268 LRWHAVPVISNMRLRIGG (SEQ ID NO: 21) 270-286 DYPLAPFNGWYMGTEIG (SEQ ID NO: 22) 288-293 RNLVDE (SEQ ID NO: 23) 299-333 LPAVAACLQLDTTSESTLWRDRALVELNVAVLHSF (SEQ ID NO: 24) 335-354 AAGVRISDHHEESRRFLAHL (SEQ ID NO: 25) 356-364 KEERQGRTV (SEQ ID NO: 26) 366-389 ADWSWIVPPLSGGITPVFHRYYDN (SEQ ID NO: 27) 391-400 DQRPNFYPHQ (SEQ ID NO: 28) ¹The “Location” refers to the range of amino acid residues as corresponding to the amino acid seguence of the NOS from Streptomyces acidiscabies (i.e., SEQ ID NO: 2).

Thus, one aspect of the present invention includes an isolated nucleic acid molecule that encode a NOS protein or polypeptide having an amino acid motif having an amino acid sequence of one of the following: SEQ ID NO:7; SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:12; SEQ ID NO:13; SEQ ID NO:14; SEQ ID NO:15; SEQ ID NO:16; SEQ ID NO:17; SEQ ID NO:18; SEQ ID NO:19; SEQ ID NO:20; SEQ ID NO:21; SEQ ID NO:22; SEQ ID NO:23; SEQ ID NO:24; SEQ ID NO:25; SEQ ID NO:26; SEQ ID NO:27; SEQ ID NO:28; and/or combinations thereof.

The information presented in Table 1 can be combined to define a NOS protein or polypeptide of the present invention as having an amino acid sequence of SEQ ID NO:47 (with X being any amino acid) as follows: (3X-49X) EVALGPSLPAPSPTACPAL (7X) PVPSAEPAT (3X) CGVADP (1X) EAEEFLRQFHAE QSDQ (9X) QVRAAIDATGTYRHTTAELV (1X) GARVAWRNSSRCIGRLYWNSLRVLDRRD (6X) IH RHLCTHLRQATNGGRIRPVISVFAPD (8X) VWNEQL (6X) RRDDGTVLGDPR (1X) ADLTEAI (2X) LGWQG (2X) QGPFDVLPLVID (2X) DDKPRFFELPRE (1X) VLEVPITHPDVPRLAEL (1X) LRWHAVPVISNMRLRIGG (1X) DYPLAPFNGWYMGTEIG (1X) RNLVDE (5X) LPAVAACLQLDTT SESTLWRDRALVELNVAVLHSF (1X) AAGVRISDHHEESRRFLAHL (1X) KEERQGRTV (1X) ADW SWIVPPLSGGITPVFHRYYDN (1X) DQRPNFYPHQ

Mutations or variants of the above polypeptides or proteins are encompassed by the present invention. Variants may be made by, for example, the deletion or addition of amino acids that have minimal influence on the properties, secondary structure, and hydropathic nature of a polypeptide or protein. For example, a polypeptide may be conjugated to a signal (or leader) sequence at the N-terminal end of the protein which co-translationally or post-translationally directs transfer of the protein. The polypeptide may also be conjugated to a linker or other sequence for ease of synthesis, purification, or identification of the polypeptide.

Also suitable as an isolated nucleic acid molecule according to the present invention is a nucleic acid molecule having a nucleotide sequence that is at least 55 percent similar, particularly at least 85 percent similar, and more particularly at least 90 percent similar to the nucleotide sequence of SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5 by basic BLAST using default parameters analysis. Another suitable isolated nucleic acid of the present invention is one having a nucleotide sequence having at least 60 percent homology, particularly at least 70 percent homology, more particularly at least 80 percent homology, more particularly at least 90 percent homology, and still more particularly at least 95 percent homology to a nucleic acid according to SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5.

Suitable nucleic acid molecules also include those that hybridize to a nucleic acid molecule comprising a nucleotide sequence of SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5 under stringent conditions. For the purposes of defining the level of stringency, reference can conveniently be made to Sambrook et al., Molecular Cloning: a Laboratory Manual, 2^(nd) Edition, Cold Spring Harbor, N.Y., Cold Spring Harbor Laboratory Press, at 11.45 (1989), which is hereby incorporated by reference in its entirety). An example of low stringency conditions is 4-6×sodium citrate (“SSC”)/0.1-0.5% w/v SDS at 37°-45° C. for 2-3 hours. Depending on the source and concentration of the nucleic acid involved in the hybridization, alternative conditions of stringency may be employed such as medium stringent conditions. Examples of medium stringent conditions include 1-4×SSC/0.25% w/v SDS at ≧45° C. for 2-3 hours. An example of high stringency conditions includes 0.1-1×SSC/0.1% w/v SDS at 60° C. for 1-3 hours. The skilled artisan is aware of various parameters which may be altered during hybridization and washing and which will either maintain or change the stringency conditions. Other examples of high stringency conditions include: 4-5×SSC/0.1% w/v SDS at 54° C. for 1-3 hours and 4×SSC at 65° C., followed by a washing in 0.1×SSC at 65° C. for about one hour. Alternatively, an exemplary stringent hybridization condition is in 50% formamide, 4×SSC, at 42° C. Still another example of stringent conditions include hybridization at 62° C. in 6×SSC, 0.05×BLOTTO, and washing at 2×SSC, 0.1% SDS at 62° C. In one particular embodiment, the stringent conditions are characterized by a hybridization medium including about 5×SSC at a temperature of about 55° C.

The precise conditions for any particular hybridization are left to those skilled in the art because there are variables involved in nucleic acid hybridizations beyond those of the specific nucleic acid molecules to be hybridized that affect the choice of hybridization conditions. These variables include: the substrate used for nucleic acid hybridization (e.g., charged vs. non-charged membrane); the detection method used (e.g., radioactive vs. chemiluminescent); and the source and concentration of the nucleic acid involved in the hybridization. All of these variables are routinely taken into account by those skilled in the art prior to undertaking a nucleic acid hybridization procedure.

A nitric oxide synthase protein or polypeptide of the present invention is preferably produced in purified form (e.g., at least about 80 percent, more preferably 90 percent pure) by conventional techniques. For example, a nitric oxide synthase protein or polypeptide of the present invention may be secreted into the growth medium of recombinant host cells. To isolate the nitric oxide synthase protein or polypeptide, a protocol involving a host cell such as Escherichia coli may be used, in which protocol the E. coli host cell carrying a recombinant plasmid is propagated, homogenized, and the homogenate is centrifuged to remove bacterial debris. The supernatant is then subjected to sequential ammonium sulfate precipitation. The fraction containing the nitric oxide synthase protein or polypeptide of the present invention is subjected to gel filtration in an appropriately sized dextran or polyacrylamide column to separate the proteins or polypeptides. If necessary, the protein fraction may be further purified by high performance liquid chromatography (“HPLC”).

The present invention relates to a DNA construct that contains a DNA molecule encoding for a nitric oxide synthase protein or polypeptide of the present invention. This involves incorporating one or more of the nucleic acid molecules of the present invention, or a suitable portion thereof, into host cells using conventional recombinant DNA technology. Generally, this involves inserting the nucleic acid molecule into an expression system to which the nucleic acid molecule is heterologous (i.e., not normally present). The expression system contains the necessary elements for the transcription and translation of the inserted protein-coding sequences.

The present invention also relates to an expression system (e.g., an expression vector) containing a nucleic acid molecule encoding a nitric oxide synthase protein or polypeptide of the present invention. The nucleic acid molecules of the present invention may be inserted into any of the many available expression vectors and cell systems using reagents that are well known in the art. In preparing a DNA vector for expression, the various DNA sequences may normally be inserted or substituted into a bacterial plasmid. Any convenient plasmid may be employed, which will be characterized by having a bacterial replication system, a marker which allows for selection in a bacterium, and generally one or more unique, conveniently located restriction sites. Numerous plasmids, referred to as transformation vectors, are available for transformation. The selection of a vector will depend on the preferred transformation technique and target cells for transfection.

Suitable vectors include, but are not limited to, the following viral vectors such as lambda vector system gt11, gt WES.tB, Charon 4, and plasmid vectors such as pBR322, pBR325, pACYC177, pACYC1084, pUC8, pUC9, pUC18, pUC19, pLG339, pR290, pKC37, pKC101, SV 40, pBluescript II SK+/− or KS+/− (see “Stratagene Cloning Systems” Catalog (1993) from Stratagene, La Jolla, Calif., which is hereby incorporated by reference in its entirety), pQE, pIH821, pGEX, pET series (see F. W. Studier et. al., “Use of T7 RNA Polymerase to Direct Expression of Cloned Genes,” Gene Expression Technology, Vol. 185 (1990), which is hereby incorporated by reference in its entirety), pCB201, and any derivatives thereof. Any appropriate vectors now known or later described for genetic transformation are suitable for use with the present invention. Recombinant molecules can be introduced into cells via transformation, particularly transduction, conjugation, mobilization, or electroporation. The DNA sequences are cloned into the vector using standard cloning procedures in the art, as described by Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N.Y. (1989), and Ausubel, F. M. et al. (1989) Current Protocols in Molecular Biology, John Wiley & Sons, New York, N.Y., which are hereby incorporated by reference in their entirety.

U.S. Pat. No. 4,237,224 issued to Cohen and Boyer, which is hereby incorporated by reference in its entirety, describes the production of expression systems in the form of recombinant plasmids using restriction enzyme cleavage and ligation with DNA ligase. These recombinant plasmids are then introduced by means of transformation and replicated in unicellular cultures including prokaryotic organisms and eukaryotic cells grown in tissue culture.

A variety of host-vector systems may be utilized to express the protein-encoding sequence(s). Primarily, the vector system must be compatible with the host cell used. Host-vector systems include but are not limited to the following: bacteria transformed with bacteriophage DNA, plasmid DNA, or cosmid DNA; microorganisms such as yeast containing yeast vectors; mammalian cell systems infected with virus (e.g., vaccinia virus, adenovirus, etc.); insect cell systems infected with virus (e.g., baculovirus); and plant cells infected by bacteria. The expression elements of these vectors vary in their strength and specificities. Depending upon the host-vector system utilized, any one of a number of suitable transcription and translation elements can be used.

Thus, certain “control elements” or “regulatory sequences” are also incorporated into the plasmid-vector constructs of the present invention. These include non-transcribed regions of the vector and 5′ and 3′ untranslated regions, which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and/or translation elements, including constitutive, inducible, and repressible promoters, as well as minimal 5′ promoter elements may be used. A constitutive promoter is a promoter that directs expression of a gene throughout the development and life of an organism. An inducible promoter is a promoter that is capable of directly or indirectly activating transcription of one or more DNA sequences or genes in response to an inducer. In the absence of an inducer, the DNA sequences or genes will not be transcribed or will only be minimally transcribed.

The DNA sequences of eukaryotic promoters differ from those of prokaryotic promoters. Furthermore, eukaryotic promoters and accompanying genetic signals may not be recognized in or may not function in a prokaryotic system, and, further, prokaryotic promoters are not recognized and do not function in eukaryotic cells.

Promoters vary in their “strength” (i.e. their ability to promote transcription). For the purposes of expressing a cloned gene, it is desirable to use strong promoters in order to obtain a high level of transcription and, hence, expression of the gene. Depending upon the host cell system utilized, any one of a number of suitable promoters may be used. For instance, when cloning in E. coli, its bacteriophages, or plasmids, promoters such as the T7 phage promoter, lac promoter, trp promoter, recA promoter, ribosomal RNA promoter, the P_(R) and P_(L) promoters of coliphage lambda and others, including but not limited, to lacUV5, ompF, bla, lpp, and the like, may be used to direct high levels of transcription of adjacent DNA segments. Additionally, a hybrid trp-lacUV5 (tac) promoter or other E. coli promoters produced by recombinant DNA or other synthetic DNA techniques may be used to provide for transcription of the inserted gene.

Other examples of some constitutive promoters that are widely used for inducing expression of transgenes include the nopoline synthase gene promoter from Agrobacterium tumefaciens (U.S. Pat. No. 5,034,322 issued to Rogers et al., which is hereby incorporated by reference in its entirety), the cauliflower mosaic virus (CaMV) 35S and 19S promoters (U.S. Pat. No. 5,352,605 issued to Fraley et al., which is hereby incorporated by reference in its entirety), the enhanced CaMV35S promoter (“enh CaMV35S”), the figwort mosaic virus full-length transcript promoter (“FMV35S”), those derived from any of the several actin genes, which are known to be expressed in most cells types (U.S. Pat. No. 6,002,068 issued to Privalle et al., which is hereby incorporated by reference in its entirety), and the ubiquitin promoter, which is a gene product known to accumulate in many cell types. Examples of constitutive promoters for use in mammalian cells include the RSV promoter derived from Rous sarcoma virus, the CMV promoter derived from cytomegalovirus, β-actin and other actin promoters, and the EF1α promoter derived from the cellular elongation factor 1α gene.

Bacterial host cell strains and expression vectors may be chosen which inhibit the action of the promoter unless specifically induced. In certain operations, the addition of specific inducers is necessary for efficient transcription of the inserted nucleic acid. For example, the lac operon is induced by the addition of lactose or IPTG (isopropylthio-beta-D-galactoside). A variety of other operons, such as trp, pro, etc., are under different controls.

Other examples of some inducible promoters, induced, for examples by a chemical agent, such as a metabolite, growth regulator, herbicide or phenolic compound, or a physiological stress/physical means, such as cold, heat, salt, toxins, or through the action of a pathogen or disease agent such as a virus or fungus, include a glucocorticoid-inducible promoter (Schena et al., Proc. Natl. Acad. Sci. 88:10421-5 (1991), which is hereby incorporated by reference in its entirety), the heat shock promoter (“Hsp”), IPTG or tetracycline (“Tet on” system), the metallothionine promoter, which is activated by heavy metal ions, and hormone-responsive promoters, which are activated by treatment of certain hormones. A host cell containing an inducible promoter may be exposed to an inducer by externally applying the inducer to the cell. In addition, “tissue-specific” promoters can be used, which are promoters that function in a tissue specific manner to regulate the gene of interest within selected tissues of the host. Examples of such tissue specific promoters include seed, flower, or root specific promoters as are well known in the field (e.g., U.S. Pat. No. 5,750,385 to Shewmaker et al., which is hereby incorporated by reference in its entirety). Promoters of the nucleic acid construct of the present invention may be either homologous (derived from the same species as the host cell) or heterologous (derived from a different species than the host cell).

Specific initiation signals are also required for efficient gene transcription and translation in prokaryotic cells. These transcription and translation initiation signals may vary in “strength” as measured by the quantity of gene specific messenger RNA and protein synthesized, respectively. The DNA expression vector, which contains a promoter, may also contain any combination of various “strong” transcription and/or translation initiation signals. For instance, efficient translation in E. coli requires an SD sequence about 7-9 bases 5′ to the initiation codon (“ATG”) to provide a ribosome binding site. Thus, any SD-ATG combination that can be utilized by host cell ribosomes may be employed. Such combinations include but are not limited to the SD-ATG combination from the cro gene or the N gene of coliphage lambda, or from the E. coli tryptophan E, D, C, B or A genes. Additionally, any SD-ATG combination produced by recombinant DNA or other techniques involving incorporation of synthetic nucleotides may be used.

The constructs of the present invention also include an operable 3′ regulatory region, selected from among those which are capable of providing correct transcription termination and polyadenylation of mRNA for expression in the host cell of choice, operably linked to a DNA molecule which encodes for a protein of choice. A number of 3′ regulatory regions are known in the art. Virtually any 3′ regulatory region known to be operable in the host cell of choice would suffice for proper expression of the coding sequence of the nucleic acid of the present invention.

In one aspect of the present invention, the nucleic acid molecule of the present invention is incorporated into an appropriate vector in the sense direction, such that the open reading frame is properly oriented for the expression of the encoded protein under control of a promoter of choice. This involves the inclusion of the appropriate regulatory elements into the DNA-vector construct. These include non-translated regions of the vector, useful promoters, and 5′ and 3′ untranslated regions which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used.

A nucleic acid molecule of the preset invention, promoter of choice, an appropriate 3′ regulatory region, and, if desired, a reporter gene, can be incorporated into a vector-expression system to contain a nucleic acid of the present invention, or a suitable fragment thereof, using standard cloning techniques as described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press, NY (1989), and Ausubel et al. (1989) Current Protocols in Molecular Biology, John Wiley & Sons, New York, N.Y., which are hereby incorporated by reference in their entirety. The transcriptional and translational elements are operably linked to the nucleic acid molecule of the present invention or a fragment thereof, meaning that the resulting vector expresses the nitric oxide synthase protein or polypeptide when placed in a suitable host cell.

Once an isolated DNA molecule encoding a nitric oxide synthase protein or polypeptide has been cloned into an expression vector, it is ready to be incorporated into a host cell. Such incorporation can be carried out by the various forms of transformation noted above, depending upon the vector/host cell system. Recombinant molecules can be introduced into cells via transformation, particularly transduction, conjugation, mobilization, or electroporation. The nucleic acid sequences are cloned into the host cell using standard cloning procedures known in the art, as described by Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Springs Laboratory, Cold Springs Harbor, N.Y. (1989), which is hereby incorporated by reference in its entirety. Suitable host cells include, but are not limited to, bacteria, virus, yeast, mammalian cells, insect, plant, and the like. Examples of a suitable bacterial host cells include, without limitation, Streptomyces, Bacillus, Escherichia, Brevibacterium, Microbacterium, Nocardia, and Rhodococcus cells. Particular Streptomyces host cells can include Streptomyces acidiscabies, Streptomyces scabies, Streptomyces turgidiscabies, Streptomyces avermitilis, Streptomyces lividans, Streptomyces coelicolor, and Streptomyces ipomoea. Particular Escherichia host cells can include Escherichia coli. Particular Bacillus host cells can include Bacillus subtilis, Bacillus anthracis, Bacillus cereus, and Bacillus halodurans. Examples of suitable fungal host cells include, without limitation, Aspergillus, Cephalosporium, and Penicillium cells. Suitable yeast host cells include, with limitation, Saccharomyces cells.

Thus, the present invention also relates to a host cell incorporating one or more of the isolated nucleic acid molecules of the present invention. In one embodiment, the isolated nucleic acid molecule is heterologous to the host cell. Such incorporation can be carried out by the various forms of transformation noted above, depending upon the vector/host system, and using the various host cells described above.

Methods of transformation may result in transient or stable expression of the DNA under control of the promoter. Preferably, the nucleic acid of the present invention is stably inserted into the genome of the host cell as a result of the transformation, although transient expression can serve an important purpose.

The present invention also relates to a method of attaching a nitrogen group to a target moiety of a compound. This method involves providing a nitric oxide synthase. The method also involves providing a compound having a target moiety to which can be attached a nitrogen group. The nitric oxide synthase and the compound are combined in a reaction mixture under conditions effective to allow the nitric oxide synthase to catalyze a reaction whereby a nitrogen group contained in the reaction mixture is attached to the target moiety. The method thereby yields a nitrogen-modified compound.

The present invention further relates to a method of synthesizing a nitrogen-modified compound in a transgenic host cell. This method involves providing a transgenic host cell transformed with a DNA molecule encoding a nitric oxide synthase. A non-modified compound containing a target moiety is also provided. The transgenic host cell and the non-modified compound are cultured in a culture medium under conditions effective to allow the nitric oxide synthase to be expressed and to catalyze a reaction whereby a nitrogen group contained in the host cell or culture medium attaches to the target moiety. The method thereby yields a nitrogen-modified compound. The non-modified compound containing a target moiety can be provided exogenously. Alternatively, the non-modified compound containing a target moiety can be produced by the transgenic host cell. Suitable DNA molecules include those of the present invention, as well as those encoding the various nitric oxide synthases described herein (and as specifically identified infra).

As used herein, the term “Nitrogen-Modifying Methods” refers to the above-referenced “method of attaching a nitrogen group to a target moiety of a compound” and “method of synthesizing a nitrogen-modified compound in a transgenic host cell.” Suitable host cells, nitrogen groups, target moieties, and nitrogen-modified compounds for use in the Nitrogen-Modifying Methods of the present invention are further described below.

In one example for conducting the Nitrogen-Modifying Methods of the present invention, the NOS-mediated nitration and/or nitrosylation can proceed by incubating the compound (e.g., molecule) having the target moiety targeted for modification with the following: (i) a nitric oxide synthase of the present invention (which functions as a catalyst for nitration and/or nitrosylation); (ii) a nitrogen-containing substrate for NOS (also referred to herein as the “NOS substrate”); and (iii) a source of oxygen (e.g., reduced oxygen). A suitable NOS substrate can include any nitrogen-containing molecule that can bind at the NOS heme center and be converted to an oxidized form of nitrogen capable of nitration and/or nitrosylation reactions. For example, the NOS substrate can contain either a guanidinum group, an hydroxy-guanidinium group, and/or an oxime group. Oxygen can be supplied in the form of molecular oxygen (O₂), reduced oxygen (e.g., peroxide (O₂ ²⁻) or superoxide (O₂ ⁻)), or as an oxo-donor compound such as m-chloroperoxybenzoic acid. Depending on the oxygen and nitrogen-containing substrate used, additional reducing equivalents may be provided in the form of small molecule electron donors (e.g., dithionite, reduced methyl viologen) or as a reductase protein (e.g., iron-sulfur cluster, heme, or flavin-containing enzymes).

Suitable nitric oxide synthases for use in the Nitrogen-Modifying Methods of the present invention can include any nitric oxide synthase (from any source) that can function as a catalyst in a nitration and/or nitrosylation reaction. Examples of such suitable nitric oxide synthases are those described herein and/or encoded by the isolated nucleic acid molecules of the present invention (described supra). Other suitable examples of nitric oxide synthases or nucleic acid molecules for use in the Nitrogen-Modifying Methods include those that have (or encode) the following three conserved amino acid regions (i.e., motifs): (i) the RCIGR (SEQ ID NO:44) motif (corresponding to amino acid residues 105-109 of the nitric oxide synthase of Streptomyces acidiscabies (SEQ ID NO:2)), which functions to coordinate the iron of the heme prosthetic group; (ii) the GWYXXXE (SEQ ID NO:45, where X can be any amino acid residue) motif (corresponding to amino acid residues 278-284 of the nitric oxide synthase of Streptomyces acidiscabies (SEQ ID NO:2)), which functions to bind the guanidinium or hydroxy-guanidinium-containing NOS substrate; and (iii) the WSWXXXP (SEQ ID NO:46, where X can be any amino acid residue) motif (corresponding to amino acid residues 368-374 of the nitric oxide synthase of Streptomyces acidiscabies (SEQ ID NO:2)), which functions to interact with cofactors or substrates that can be capable of reduction/oxidaton reactions with the NOS heme center (e.g. reduced pterins such as tetrahydrofolateand tetrahydrobiopterin). The three conserved motifs described above can be combined to define a nitric oxide synthase protein or polypeptide for use in the Nitrogen-Modifying Methods of the present invention as having an amino acid sequence of SEQ ID NO:50 as follows: (37X-174X) RCIGR (48X-67X) GWYXXXE (83X) WSWXXXP (20X-38X)

Still other suitable nitric oxide synthases for use in Nitrogen-Modifying Methods can include those having amino acid sequences that contain amino acid motifs that are conserved in nitric oxide synthases from a variety of sources. Suitable sources of nitric oxide synthases can include, for example, Bacillus anthracis, Bacillus cereus, Bacillus subtilis, Bacillus halodurans, Staphylococcus aureus, Staphylococcus epidermidis, Deinococcus radiodurans, Mus musculus, Streptomyces acidiscabies, Streptomyces scabies Streptomyces turgidiscabies, and Streptomyces avermitilis. An alignment of the nitric oxide synthases from these organisms is shown in FIG. 6.

The various conserved regions of the nitric oxide synthases from Streptomyces acidiscabies, Streptomyces scabies Streptomyces turgidiscabies, and Streptomyces avermitilis are described below in Table 2 (below). TABLE 2 Conserved Regions of the Nitric Oxide Synthase Proteins or Polypeptides From Streptomyces acidiscabies, Streptomyces scabies, Streptomyces turgidiscabies, and Streptomyces avermitilis Location¹ Motif 82-89 TGTYRHTT (SEQ ID NO: 29)  95-102 GARVAWRN (SEQ ID NO: 30) 105-112 RCIGRLYW (SEQ ID NO: 31) 152-156 VFAPD (SEQ ID NO: 32) 166-170 WNEQL (SEQ ID NO: 33) 208-214 PFDVLPL (SEQ ID NO: 34) 251-257 LRWHAVP (SEQ ID NO: 35) 274-286 APFNGWYMGTEIG (SEQ ID NO: 36) 319-326 DRALVELN (SEQ ID NO: 37) 329-333 VLHSF (SEQ ID NO: 38) 366-374 ADWSWIVPP (SEQ ID NO: 39) 380-385 TPVFHR (SEQ ID NO: 40) ¹The “Location” refers to the range of amino acid residues as corresponding to the amino acid seguence of the NOS from Streptomyces acidiscabies (i.e., SEQ ID NO: 2).

The information presented in Table 2 can be combined to define a nitric oxide synthase protein or polypeptide for use in the Nitrogen-Modifying Methods of the present invention as having an amino acid sequence of SEQ ID NO:48 (with X being any amino acid) as follows: (81X-151X)TGTYRHTT(5X)GARVAWRN(2X)RCIGRLYW(39X)VFAPD(9X)WNEQL(37X) PFDVLPL(36X)LRWHAVP(16X)APFNGWYMGTEIG(32X)DRALVELN(2X)VLHSF(32X)AD WSWIVPP(5X)TPVFHR(15X-30X)

The various conserved regions of the nitric oxide synthases from Bacillus anthracis, Bacillus cereus, Bacillus subtilis, Staphylococcus aureus, Staphylococcus epidermidis, Deinococcus radiodurans, Mus musculus, Streptomyces acidiscabies, Streptomyces scabies Streptomyces turgidiscabies, and Streptomyces avermitilis are described below in Table 3 (below). TABLE 3 Conserved Regions of the Nitric Oxide Synthase Proteins or Polypeptides From Eleven Different Sources³ Location¹ Motif²  97-103 23AWRN4 (SEQ ID NO:41) 105-110 RC5GR6 (SEQ ID NO:42) 169-174 QL5RYA (SEQ ID NO:43) ¹The “Location” refers to the range of amino acid residues as corresponding to the amino acid sequence of the NOS from Streptomyces acidiscabies (i.e., SEQ ID NO:2). ²The numerals used in the Motifs represent alternative amino acid residues as follows: 2 = R or K; 3 = M or V; 4 = S or A; 5 = I or V; and 6 = L or I ³The twelve sources include Bacillus anthracis, Bacillus cereus, Staphylococcus aureus, Staphylococcus epidermidis, Bacillus halodurans, Bacillus subtilis subsp. subtilis, Deinococcus radiodurans, Streptomyces acidiscabies, Streptomyces scabies, Streptomyces turgidiscabies, Streptomyces avermitilis, and Mus musculus.

The information presented in Table 3 can be combined to define a nitric oxide synthase protein or polypeptide for use in the Nitrogen-Modifying Methods of the present invention as having an amino acid sequence of SEQ ID NO:49 (with X being any amino acid and 2, 3, 4, 5 and 6 having the same definitions as for Table 3) as follows: (29X-166X)23AWRN4(1X)RC5GR6(52X-58X)QL5RYA(220X- 243X)

In view of the information contained herein regarding conserved regions of the various nitric oxide synthases, a suitable nitric oxide synthase for use in the Nitrogen-Modifying Methods of the present invention can include proteins or polypeptides having an amino acid motif having an amino acid sequence of one of the following: SEQ ID NO:7; SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:12; SEQ ID NO:13; SEQ ID NO:14; SEQ ID NO:15; SEQ ID NO:16; SEQ ID NO:17; SEQ ID NO:18; SEQ ID NO:19; SEQ ID NO:20; SEQ ID NO:21; SEQ ID NO:22; SEQ ID NO:23; SEQ ID NO:24; SEQ ID NO:25; SEQ ID NO:26; SEQ ID NO:27; SEQ ID NO:28; SEQ ID NO:29; SEQ ID NO:30; SEQ ID NO:31; SEQ ID NO:32; SEQ ID NO:33; SEQ ID NO:34; SEQ ID NO:35; SEQ ID NO:36; SEQ ID NO:37; SEQ ID NO:38; SEQ ID NO:39; SEQ ID NO:40; SEQ ID NO:41; SEQ ID NO:42; SEQ ID NO:43; SEQ ID NO:44; SEQ ID NO:45; SEQ ID NO:46; and/or combinations thereof. More particularly, the nitric oxide synthase used in the Nitrogen-Modifying Methods of the present invention can have an amino acid sequence of SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, or SEQ ID NO:50.

As referenced in the Nitrogen-Modifying Methods of the present invention, a suitable nitrogen group can include a nitro group (i.e., NO₂) or a nitroso group (i.e., NO). The reaction catalyzed by the nitric oxide synthase, whereby the nitrogen group is added to the target moiety, can be a nitration reaction or a nitrosylation reaction.

The Nitrogen-Modifying Methods of the present invention can be used to yield various types of nitrogen-modified compounds. An example of a class of nitrogen-modified compounds of the present invention are secondary metabolites. As used herein, the term “secondary metabolite” refers to those compounds of an organism that are not essential for normal growth, development, or reproduction of that organism. Suitable examples of such secondary metabolites include alkaloids, terpenoids, aliphatic organic acids, aromatic organic acids, heteroaromatic organic acids, phenols, irridoids, steroids, volatile oils, resins, balsams, β-lactams, aminoglycosides, macrolides, tetracyclines, and saponins. Other suitable nitrogen-modified compounds can include polyketides, peptides (including, for example, non-ribosomal peptides), and phytotoxins (including, for example, thaxtomin). Still other suitable nitrogen-modified compounds can include herbicides, nematicides, fungicides, insecticides, antibiotics (e.g., chloramphenicol), and anticancer agents (e.g., L-alanosine). Additional suitable nitrogen-modified compounds can include high-energy materials. Examples of such high-energy materials include nitroglycerin, trinitrotoluene, pentaerythriotoltetranitrate, cyclotrimethylenetrinitramine, and ammonium nitrate fertilizer.

Various moieties of compounds can be targeted for addition of a nitrogen group. An example of a target moiety (as defined by the present invention) can include an electron-rich aromatic group. Particular target moieties can include a phenyl moiety or an indole moiety, and more particularly a tryptophanyl moiety.

EXAMPLES Example 1 Thaxtoniin Production

Streptomyces turgidiscabies cultures were grown in oat bran broth or oat meal broth (Healy et al., Mol. Micro. 38:794-804 (2000); and Goyer et al., Phytopathology 88:442-445 (1998), which are hereby incorporated by reference in their entirety) inoculated with spores. After shaking at 150 rpm and 25° C. for 5-9 days the cultures were filtered and dry weight of the mycelia was measured. Thaxtomin was extracted from the filtrate with ethyl acetate, dried, redissolved in methanol, and quantified using HPLC (column: 5 μm C18; 250×4.6 mm; mobile phase: MeCN: H₂0:TFA (40:60:0.1)). In experiments investigating the suppression of thaxtomin production in the presence of L-NAME, this NOS inhibitor was dissolved in water, filter-sterilized, and added at the time of inoculation.

Example 2 ¹⁵N Feeding Studies

NMR analysis was conducted on thaxtomin A extracted from cultures fed either L-Arginine-guanidino-¹⁵N₂.HCl (Cambridge Isotope Laboratories), or ¹⁵NH₄NO₃ (Aldrich). ¹⁵NH₄NO₃ was added to oat bran broth at the time of inoculation with spores of S. turgidiscabies, whereas L-Arg-guanidino-¹⁵N₂.HCl was added just prior to the onset of thaxtomin biosynthesis (4-5 days after inoculation). Purified thaxtomin A dissolved in CD₃OD was analyzed on a Varian VXR-400S spectrometer equipped with a Nalorac broad-band probe affording observation of ¹⁵N at 40.5 MHZ. Spectra were referenced externally by observing the ¹⁵N signal of formamide (90% solution in DMSO) and then acquiring sample spectra with identical parameter sets. A conventional chemical shift scale (liquid NH₃=0 ppm) was established by referencing the formamide signal to its reported value of 112 ppm (Martin et al., J. Nat. Prod. 63:543-585 (2000), which is hereby incorporated by reference in its entirety).

Example 3 Molecular Biology

DNA and RNA manipulation were performed using standard techniques. Transformation of S. turgidiscabies was performed using polyethylene glycol (PEG) mediated transformation of S. turgidiscabies protoplasts using plasmid vectors propagated in E. coli ET12567 (MacNeil et al., Gene 111:61-68 (1992), which is hereby incorporated by reference in its entirety). Streptomyces turgidiscabies p2XNOS single cross-over transformants (apramycin resistant, thiostrepton resistant) were grown for three generations of growth and sporulation on minimal medium containing thiostrepton, after which colonies containing double cross-over (apramycin sensitive, thiostrepton resistant) recombination events were screened. Expression of nos was induced in the complemented Δnos strain by addition of 10 μg ml⁻¹ thiostrepton in a 5 mL oat bran culture 3 days following inoculation.

Example 4 A Bacterial Nitric Oxide Synthase Functions to Nitrate a Peptide Phytotoxin

Plant pathogenic Streptomyces species are the causal agents of potato scab disease, a globally important disease of potato. Pathogenicity depends on production of a class of dipeptide phytotoxins called thaxtomins (Healy et al., Mol. Micro. 38:794-804 (2000), which is hereby incorporated by reference in its entirety). While investigating the molecular genetics of plant pathogenicity in Streptomyces species, it was discovered that a gene with high sequence similarity to mammalian and bacterial NOSs. The location of this gene on a pathogenicity island that mobilizes among species to confer thaxtomin biosynthetic ability and its proximity to two nonribosomal peptide synthases of the thaxtomin biosynthetic pathway suggests that the NOS participates in nitration of thaxtomins (FIG. 1A-1B). The DNA sequence of the nos genes in S. turgidiscabies, S. acidiscabies and S. scabies, all of which produce thaxtomin A, is highly conserved (Genbank accessions AY204507-AY204509). Conservation of nearly all key residues known in mammalian and B. subtilis NOSs that participate in cofactor-binding, substrate-binding and catalysis by S. turgidiscabies NOS (stNOS) suggests that stNOS is capable of producing NO from L-Arg (FIG. 2). As in other bacterial NOSs, the reductase domain and CaM binding site typical of mammalian NOSs are absent in stNOS. However, stNOS has an extended N-terminal region that is lacking in other bacterial proteins (FIG. 2). A mammalian NOS zinc-binding motif absent in the N-termini of other bacterial NOSs may be conserved in some of the pathogenic Streptomyces spp. NOSs.

To determine if stNOS is required for production of thaxtomin A, nos was deleted from S. turgidiscabies (FIGS. 3A-3B). The Δnos strain produced only trace amounts of thaxtomin A (0.20±0.02 μg ml⁻¹; standard deviation reported, n=3 for each strain tested) compared to the wild-type strain (18.31±0.92 μg ml⁻¹). De-nitrothaxtomin was not detectable in the medium. Deletion of nos did not affect bacterial growth, but did eliminate disease on potato tubers. Complemention of nos was achieved by expressing nos using the thiostrepton-inducible promoter on plasmid pIJ8600, which integrates into the chromosomal φC31 phage attachment site (FIG. 3B) (Sun et al., Microbiology 145:2221-2227 (1999), which is hereby incorporated by reference in its entirety). The complemented strain Δnos pIJ8600NOS increased the amount of thaxtomin A produced over 25 fold (3.68±0.06 μg ml⁻¹ thaxtomin A) compared to the empty vector control strain Δnos pIJ8600 (0.13±0.01 μg ml⁻¹). Expression of nos in the S. turgidiscabies wild-type strain was confirmed using reverse transciptase (RT)-PCR (FIG. 3C). nos was not expressed in the Δnos or Δnos pIJ8600 strains, but expression was restored in the complemented strain Δnos pIJ8600NOS.

For stNOS to be responsible for thaxtomin nitration, stNOS should have NO synthase activity. Further, this activity and thaxtomin production should be arginine dependent. As predicted, overexpressed stNOS in E. coli produced nitrite from N-hydroxy-L-arginine in a standard NOS assay (FIGS. 4A-4B). N-hydroxy-L-arginine is an intermediate unique to the NOS catalytic reaction and nitrite represents the end product of NO reacting in oxygenated solution. NO synthase activity of the recombinant stNOS was inhibited by the selective NOS inhibitor nitro-L-arginine (FIG. 4B); nitro-L-arginine is the active form of Nitro-L-arginine methyl ester (NAME). NOS inhibitors were also evaluated for their effect on thaxtomin A production by S. turgidiscabies. NAME greatly suppressed thaxtomin production by S. turgidiscabies (IC₅₀=15 μM) but did not affect bacterial growth (FIG. 4C). Inhibition of thaxtomin production occurred at concentrations commensurate with the binding affinities of NAME to mammalian NOSs (Alderton et al., Biochem J. 357:593-615 (2001); and Southan et al., Biochem. Pharm. 51,383-394 (1996), which are hereby incorporated by reference in their entirety). The other three NOS inhibitors tested also suppressed thaxtomin A production but to a lesser extent than NAME. Thus, inhibitors specific for the conserved NOS active center greatly curtail both NO synthase activity from recombinant stNOS in vitro and thaxtomin production in vivo.

Mammalian NOSs convert a terminal guanidino nitrogen of the L-Arg substrate to an oxidized nitrogen species. One model for the role of stNOS in nitration of thaxtomin predicts that the nitrate nitrogen derives from a terminal guanidino nitrogen of L-Arg. A ¹⁵N feeding study was conducted; either L-Arg -guanidino-¹⁵N₂.HCI or ¹⁵NH₄NO₃ was added to cultures of S. turgidiscabies under conditions that induce thaxtomin production. ¹⁵N-NMR analysis of thaxtomin A extracted from cultures fed the L-Arg-guanidino-¹⁵N₂.HCl detected label only at the 4-nitro position, while in thaxtomin A extracted from control cultures fed ¹⁵NH₄NO₃, all of the four nitrogens in thaxtomin were equally labeled (FIGS. 5A-5B). Electron impact ionization mass spectra of thaxtomin A also indicated specific incorporation of ¹⁵N into the nitro group when the cultures were fed L -Arg-guanidino-¹⁵N₂.HCl. There is no known enzymatic process other than NOS activity that converts L-Arg terminal guanidino nitrogen to an oxidized nitrogen species capable of nitration. These results provide definitive evidence for the role of stNOS in nitration of thaxtomin.

The specific nitration of a tryptophanyl moiety for biosynthesis is an unprecedented metabolic role for a NOS protein, although mammalian NOS production of nitroxyl (NO⁻) and superoxide (O₂ ⁻) is well characterized and such products could readily lead to nitrating species (Alderton et al., Biochem J. 357:593-615 (2001), which is hereby incorporated by reference in its entirety). Biosynthetic nitration reactions are rare and usually involve the oxidation of an amine (Carter et al, J. Chem. Soc. Chem. Commun. 17:1271-1273 (1989), which is hereby incorporated by reference in its entirety). The chemical mechanism of a NOS-mediated nitration may be complex because NO is unlikely to react directly with indole (Patel et al., Biochemica. Biophys. Acta. 1411:385-400 (1999); Koppenol, Free Rad. Biol. Med. 25:385-391 (1998); Hughes, Biochim. Biophys. Acta 1411:263-272 (1999); and Ridd, Acta Chemica. Scand. 52:11-22 (1998), which are hereby incorporated by reference in their entirety). Nevertheless, readily oxidized forms of NO, such as nitrosonium (NO⁺), peroxynitrite (ONOO⁻), nitronium (NO₂ ⁺), or nitrogen dioxide (NO₂) actively nitrate aromatic amino acids (Patel et al., Biochemica. Biophys. Acta. 1411:385-400 (1999); Koppenol, Free Rad. Biol. Med. 25:385-391 (1998); Hughes, Biochim. Biophys. Acta 1411:263-272 (1999); and Ridd, Acta Chemica. Scand. 52:11-22 (1998), which are hereby incorporated by reference in their entirety), and such reactions have been implicated in mammalian signaling (Packer, Methods Enzymol. 268 (1996); and Ischiropoulos, Free Rad. Biol. Med. 33 (2002), which are hereby incorporated by reference in their entirety). Given the high reactivities of these nitrogen oxide species towards tryptophan, the substrate nitrated likely contains indole; whether this substrate is tryptophan, an immediate precursor of thaxtomin, or some other intermediate, is currently under investigation. Interestingly, tryptophan nitration by peroxynitrite results primarily in modification at the indole 6-position (Alvarez et al., Chem. Res. Toxicol. 9:390-396 (1996), which is hereby incorporated by reference in its entirety). Thus, production of a 4-nitrotryptophanyl moiety (FIG. 1A) suggests some enzymatic control of the nitration reaction. Nevertheless, minimal thaxtomin production in the Δnos strain indicates that diffusible nitration agents produced by other cellular processes can react productively with a thaxtomin precursor.

Conservation of residues in the heme pocket, pterin site, and substrate access channel among the bacterial NOSs suggest a common function for prokaryotic enzymes and distinguish them from their mammalian counterparts (FIG. 2). A distinguishing catalytic feature between mammalian NOS and bsNOS is that the bacterial protein retains product NO coordinated to its heme iron 10-20×longer than the mammalian enzymes (Adak et al., J. Biol. Chem. 277:16167-16171 (2002), which is hereby incorporated by reference in its entirety)). This correlates to a more sequestered immediate heme pocket that appears conserved in stNOS (Pant et al., Biochemistry 41:11071-11079 (2002), which is hereby incorporated by reference in its entirety). Perhaps a slower NO release allows bacterial proteins to direct NO reactivity by either sequestering NO close to the site of substrate binding, or by facilitating reaction with O₂. It is suggested that other bacterial NOSs may also participate in the biosynthesis of secondary metabolites through nitration of an amino acid or peptide substrate. Truncated NOSs have only been discovered in a subset of Gram-positive genomes and are absent from Gram-negative genomes, supporting a role for NOS proteins in secondary metabolism, rather than a signaling function essential for vitality. Nitrated compounds are produced by other bacteria and fungi (Carter et al, J. Chem. Soc. Chem. Commun. 17:1271-1273 (1989); Jalal et al., Acta Crystallography C42:733-738 (1986); and Ohba et al., J. Antibiot. 40:709-713 (1987), which are hereby incorporated by reference in their entirety) and at least one is likely to derive from an aromatic nitration reaction (Carter et al, J. Chem. Soc. Chem. Commun. 17:1271-1273 (1989), which is hereby incorporated by reference in its entirety). NOS-initiated nitrations would produce a class of compounds with unique chemical reactivity and diverse biological activities. From an evolutionary perspective, it is interesting that homologous enzymes are responsible for biosynthetic nitration reactions in bacteria and NO signaling in mammals.

Although preferred embodiments have been depicted and described in detail herein, it will be apparent to those skilled in the relevant art that various modifications, additions, substitutions, and the like can be made without departing from the spirit of the invention and these are therefore considered to be within the scope of the invention as defined in the claims which follow. 

1. An isolated nucleic acid molecule encoding a nitric oxide synthase, wherein the nucleic acid molecule: (i) comprises a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, and SEQ ID NO:5; (ii) comprises a nucleotide sequence that hybridizes to SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5 under stringent conditions characterized by a hybridization medium comprising about 5×SSC at a temperature of about 55° C.; (iii) comprises a nucleotide sequence having greater than 95 percent homology to a nucleic acid according to SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5; (iv) comprises a nucleotide sequence that encodes a nitric oxide synthase protein having an amino acid sequence that is at least 85 percent similar to either SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:6 by basic BLAST using default parameters analysis; (v) encodes a nitric oxide synthase comprising a protein or polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, and SEQ ID NO:6; (vi) encodes a nitric oxide synthase comprising a protein or polypeptide having an amino acid motif selected from the group consisting of the motif of SEQ ID NO:7, the motif of SEQ ID NO:8, the motif of SEQ ID NO:9, the motif of SEQ ID NO:10, the motif of SEQ ID NO:11, the motif of SEQ ID NO:12, the motif of SEQ ID NO:13, the motif of SEQ ID NO:14, the motif of SEQ ID NO:15, the motif of SEQ ID NO:16, the motif of SEQ ID NO:17, the motif of SEQ ID NO:18, the motif of SEQ ID NO:19, the motif of SEQ ID NO:20, the motif of SEQ ID NO:21, the motif of SEQ ID NO:22, the motif of SEQ ID NO:23, the motif of SEQ ID NO:24, the motif of SEQ ID NO:25, the motif of SEQ ID NO:26, the motif of SEQ ID NO:27, the motif of SEQ ID NO:28, and combinations thereof; or (vii) encodes a nitric oxide synthase comprising a protein or polypeptide having an amino acid sequence of SEQ ID NO:47.
 2. The isolated nucleic acid molecule according to claim 1, wherein the nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, and SEQ ID NO:5.
 3. The isolated nucleic acid molecule according to claim 1, wherein the nucleic acid molecule comprises a nucleotide sequence that hybridizes to SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5 under stringent conditions characterized by a hybridization medium comprising about 5×SSC at a temperature of about 55° C.
 4. The isolated nucleic acid molecule according to claim 1, wherein the nucleic acid molecule comprises a nucleotide sequence having greater than 95 percent homology to a nucleic acid according to SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5.
 5. The isolated nucleic acid molecule according to claim 1, wherein the nucleic acid molecule comprises a nucleotide sequence that encodes a nitric oxide synthase protein having an amino acid sequence that is at least 85 percent similar to either SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:6 by basic BLAST using default parameters analysis
 6. The isolated nucleic acid molecule according to claim 1, wherein the nucleic acid molecule encodes a nitric oxide synthase comprising a protein or polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, and SEQ ID NO:6.
 7. The isolated nucleic acid molecule according to claim 1, wherein the nucleic acid molecule encodes a nitric oxide synthase comprising a protein or polypeptide having an amino acid motif selected from the group consisting of the motif of SEQ ID NO:7, the motif of SEQ ID NO:8, the motif of SEQ ID NO:9, the motif of SEQ ID NO:10, the motif of SEQ ID NO:11, the motif of SEQ ID NO:12, the motif of SEQ ID NO:13, the motif of SEQ ID NO:14, the motif of SEQ ID NO:15, the motif of SEQ ID NO:16, the motif of SEQ ID NO:17, the motif of SEQ ID NO:18, the motif of SEQ ID NO:19, the motif of SEQ ID NO:20, the motif of SEQ ID NO:21, the motif of SEQ ID NO:22, the motif of SEQ ID NO:23, the motif of SEQ ID NO:24, the motif of SEQ ID NO:25, the motif of SEQ ID NO:26, the motif of SEQ ID NO:27, the motif of SEQ ID NO:28, and combinations thereof.
 8. The isolated nucleic acid molecule according to claim 1, wherein the nucleic acid molecule encodes a nitric oxide synthase comprising a protein or polypeptide having an amino acid sequence of SEQ ID NO:47.
 9. The isolated nucleic acid molecule according to claim 1, wherein the nitric oxide synthase is from a Streptomyces species selected from the group consisting of Streptomyces acidiscabies, Streptomyces scabies, Streptomyces turgidiscabies, Streptomyces avermitilis, and Streptomyces ipomoea.
 10. The isolated nucleic acid molecule according to claim 1, wherein the nucleic acid is DNA.
 11. An expression system comprising a vector into which is inserted the nucleic acid molecule according to claim
 1. 12. The expression system according to claim 11, wherein the nucleic acid molecule is inserted in sense orientation.
 13. A host cell comprising the nucleic acid molecule according to claim
 1. 14. The host cell according to claim 13, wherein the host cell is selected from the group consisting of a bacterial cell, a yeast cell, a fungal cell, an insect cell, a plant cell, and a mammalian cell.
 15. The host cell according to claim 14, wherein the bacterial cell is Streptomyces, Bacillus, Escherichia, Brevibacterium, Microbacterium, Nocardia, or Rhodococcus.
 16. An isolated protein or polypeptide encoded by the nucleic acid molecule according to claim
 1. 17. The isolated protein or polypeptide according to claim 16, wherein the protein or polypeptide comprises an amino acid sequence that is at least 85 percent similar to either SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:6 by basic BLAST using default parameters analysis.
 18. The isolated protein or polypeptide according to claim 16, wherein the protein or polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, and SEQ ID NO:6.
 19. The isolated protein or polypeptide according to claim 16, wherein the protein or polypeptide comprises an amino acid motif selected from the group consisting of the motif of SEQ ID NO:7, the motif of SEQ ID NO:8, the motif of SEQ ID NO:9, the motif of SEQ ID NO:10, the motif of SEQ ID NO:11, the motif of SEQ ID NO:12, the motif of SEQ ID NO:13, the motif of SEQ ID NO:14, the motif of SEQ ID NO:15, the motif of SEQ ID NO:16, the motif of SEQ ID NO:17, the motif of SEQ ID NO:18, the motif of SEQ ID NO:19, the motif of SEQ ID NO:20, the motif of SEQ ID NO:21, the motif of SEQ ID NO:22, the motif of SEQ ID NO:23, the motif of SEQ ID NO:24, the motif of SEQ ID NO:25, the motif of SEQ ID NO:26, the motif of SEQ ID NO:27, the motif of SEQ ID NO:28, and combinations thereof.
 20. The isolated protein or polypeptide according to claim 16, wherein the protein or polypeptide comprises an amino acid sequence of SEQ ID NO:47.
 21. A method of attaching a nitrogen group to a target moiety of a compound, said method comprising: providing a nitric oxide synthase; providing a compound having a target moiety; and combining the nitric oxide synthase and the compound in a reaction mixture under conditions effective to allow the nitric oxide synthase to catalyze a reaction whereby a nitrogen group contained in the reaction mixture is attached to the target moiety, thereby yielding a nitrogen-modified compound, wherein the nitric oxide synthase comprises: (i) a protein or polypeptide having an amino acid sequence that is at least 85 percent similar to either SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:6 by basic BLAST using default parameters analysis; (ii) a protein or polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, and SEQ ID NO:6; (iii) a protein or polypeptide having an amino acid motif selected from the group consisting of the motif of SEQ ID NO:7, the motif of SEQ ID NO:8, the motif of SEQ ID NO:9, the motif of SEQ ID NO:10, the motif of SEQ ID NO:11, the motif of SEQ ID NO:12, the motif of SEQ ID NO:13, the motif of SEQ ID NO:14, the motif of SEQ ID NO:15, the motif of SEQ ID NO:16, the motif of SEQ ID NO:17, the motif of SEQ ID NO:18, the motif of SEQ ID NO:19, the motif of SEQ ID NO:20, the motif of SEQ ID NO:21, the motif of SEQ ID NO:22, the motif of SEQ ID NO:23, the motif of SEQ ID NO:24, the motif of SEQ ID NO:25, the motif of SEQ ID NO:26, the motif of SEQ ID NO:27, the motif of SEQ ID NO:28, the motif of SEQ ID NO:29, the motif of SEQ ID NO:30, the motif of SEQ ID NO:31, the motif of SEQ ID NO:32, the motif of SEQ ID NO:33, the motif of SEQ ID NO:34, the motif of SEQ ID NO:35, the motif of SEQ ID NO:36, the motif of SEQ ID NO:37, the motif of SEQ ID NO:38, the motif of SEQ ID NO:39, the motif of SEQ ID NO:40, the motif of SEQ ID NO:41, the motif of SEQ ID NO:42, the motif of SEQ ID NO:43, the motif of SEQ ID NO:44, the motif of SEQ ID NO:45, the motif of SEQ ID NO:46, and combinations thereof combinations thereof; or (iv) a protein or polypeptide comprises an amino acid sequence of SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, or SEQ ID NO:50.
 22. The method according to claim 21, wherein the nitric oxide synthase comprises a protein or polypeptide having an amino acid sequence that is at least 85 percent similar to either SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:6 by basic BLAST using default parameters analysis.
 23. The method according to claim 21, wherein the nitric oxide synthase comprises a protein or polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, and SEQ ID NO:6.
 24. The method according to claim 21, wherein the nitric oxide synthase comprises a protein or polypeptide having an amino acid motif selected from the group consisting of the motif of SEQ ID NO:7, the motif of SEQ ID NO:8, the motif of SEQ ID NO:9, the motif of SEQ ID NO:10, the motif of SEQ ID NO:11, the motif of SEQ ID NO:12, the motif of SEQ ID NO:13, the motif of SEQ ID NO:14, the motif of SEQ ID NO:15, the motif of SEQ ID NO:16, the motif of SEQ ID NO:17, the motif of SEQ ID NO:18, the motif of SEQ ID NO:19, the motif of SEQ ID NO:20, the motif of SEQ ID NO:21, the motif of SEQ ID NO:22, the motif of SEQ ID NO:23, the motif of SEQ ID NO:24, the motif of SEQ ID NO:25, the motif of SEQ ID NO:26, the motif of SEQ ID NO:27, the motif of SEQ ID NO:28, the motif of SEQ ID NO:29, the motif of SEQ ID NO:30, the motif of SEQ ID NO:31, the motif of SEQ ID NO:32, the motif of SEQ ID NO:33, the motif of SEQ ID NO:34, the motif of SEQ ID NO:35, the motif of SEQ ID NO:36, the motif of SEQ ID NO:37, the motif of SEQ ID NO:38, the motif of SEQ ID NO:39, the motif of SEQ ID NO:40, the motif of SEQ ID NO:41, the motif of SEQ ID NO:42, the motif of SEQ ID NO:43, the motif of SEQ ID NO:44, the motif of SEQ ID NO:45, the motif of SEQ ID NO:46, and combinations thereof combinations thereof.
 25. The method according to claim 21, wherein the nitric oxide synthase comprises a protein or polypeptide comprises an amino acid sequence of SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, or SEQ ID NO:50.
 26. The method according to claim 21, wherein the nitrogen group is a nitro group or a nitroso group.
 27. The method according to claim 21, wherein the reaction is a nitration reaction or a nitrosylation reaction.
 28. The method according to claim 21, wherein the nitrogen-modified compound is a secondary metabolite.
 29. The method according to claim 28, wherein the secondary metabolite is selected from the group consisting of an alkaloid, a terpenoid, an aliphatic organic acid, an aromatic organic acid, a heteroaromatic organic acid, a phenol, an irridoid, a steroid, a volatile oil, a resin, a balsam, and a saponin.
 30. The method according to claim 21, wherein the nitrogen-modified compound is a polyketide.
 31. The method according to claim 21, wherein the nitrogen-modified compound is a peptide.
 32. The method according to claim 31, wherein the peptide is a non-ribosomal peptide.
 33. The method according to claim 21, wherein the nitrogen-modified compound is a phytotoxin.
 34. The method according to claim 33, wherein the phytotoxin is thaxtomin.
 35. The method according to claim 21, wherein the nitrogen-modified compound is an herbicide, an antibiotic, a nematicide, a fungicide, an insecticide, or an anticancer agent.
 36. The method according to claim 35, wherein the antibiotic is chloramphenicol.
 37. The method according to claim 35, wherein the anticancer agent is L-alanosine.
 38. The method according to claim 21, wherein the nitrogen-modified compound is a high-energy material selected from the group consisting of nitroglycerin, trinitrotoluene, pentaerythriotoltetranitrate, cyclotrimethylenetrinitramine, and ammonium nitrate fertilizer.
 39. The method according to claim 21, wherein the target moiety comprises an electron-rich aromatic group.
 40. The method according to claim 21, wherein the target moiety comprises a phenyl moiety.
 41. The method according to claim 21, wherein the target moiety comprises an indole moiety.
 42. The method according to claim 21, wherein the target moiety comprises a tryptophanyl moiety.
 43. A method of synthesizing a nitrogen-modified compound in a transgenic host cell, said method comprising: providing a transgenic host cell transformed with a DNA molecule encoding a nitric oxide synthase; providing a non-modified compound containing a target moiety; and culturing the transgenic host cell and the non-modified compound in a culture medium under conditions effective to allow the nitric oxide synthase to be expressed and to catalyze a reaction whereby a nitrogen group contained in the host cell or culture medicum attaches to the target moiety, thereby yielding a nitrogen-modified compound, wherein the DNA molecule: (i) comprises a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, and SEQ ID NO:5; (ii) comprises a nucleotide sequence that hybridizes to SEQ ID NO: 1, SEQ ID NO:3, or SEQ ID NO:5 under stringent conditions characterized by a hybridization medium comprising about 5×SSC at a temperature of about 55° C.; (iii) comprises a nucleotide sequence having greater than 95 percent homology to a nucleic acid according to SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5; (iv) comprises a nucleotide sequence that encodes a nitric oxide synthase protein having an amino acid sequence that is at least 85 percent similar to either SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:6 by basic BLAST using default parameters analysis; (v) encodes a nitric oxide synthase comprising a protein or polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, and SEQ ID NO:6; (vi) encodes a nitric oxide synthase comprising a protein or polypeptide having an amino acid motif selected from the group consisting of the motif of SEQ ID NO:7, the motif of SEQ ID NO:8, the motif of SEQ ID NO:9, the motif of SEQ ID NO:10, the motif of SEQ ID NO:11, the motif of SEQ ID NO:12, the motif of SEQ ID NO:13, the motif of SEQ ID NO:14, the motif of SEQ ID NO:15, the motif of SEQ ID NO:16, the motif of SEQ ID NO:17, the motif of SEQ ID NO:18, the motif of SEQ ID NO:19, the motif of SEQ ID NO:20, the motif of SEQ ID NO:21, the motif of SEQ ID NO:22, the motif of SEQ ID NO:23, the motif of SEQ ID NO:24, the motif of SEQ ID NO:25, the motif of SEQ ID NO:26, the motif of SEQ ID NO:27, the motif of SEQ ID NO:28, the motif of SEQ ID NO:29, the motif of SEQ ID NO:30, the motif of SEQ ID NO:31, the motif of SEQ ID NO:32, the motif of SEQ ID NO:33, the motif of SEQ ID NO:34, the motif of SEQ ID NO:35, the motif of SEQ ID NO:36, the motif of SEQ ID NO:37, the motif of SEQ ID NO:38, the motif of SEQ ID NO:39, the motif of SEQ ID NO:40, the motif of SEQ ID NO:41, the motif of SEQ ID NO:42, the motif of SEQ ID NO:43, the motif of SEQ ID NO:44, the motif of SEQ ID NO:45, the motif of SEQ ID NO:46, and combinations thereof combinations thereof; or (vii) encodes a nitric oxide synthase comprising a protein or polypeptide having an amino acid sequence of SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, or SEQ ID NO:50.
 44. The method according to claim 43, wherein the DNA molecule comprises a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, and SEQ ID NO:5.
 45. The method according to claim 43, wherein the DNA molecule comprises a nucleotide sequence that hybridizes to SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5 under stringent conditions characterized by a hybridization medium comprising about 5×SSC at a temperature of about 55° C.
 46. The method according to claim 43, wherein the DNA molecule comprises a nucleotide sequence having greater than 95 percent homology to a nucleic acid according to SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5.
 47. The method according to claim 43, wherein the DNA molecule comprises a nucleotide sequence that encodes a nitric oxide synthase protein having an amino acid sequence that is at least 85 percent similar to either SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:6 by basic BLAST using default parameters analysis
 48. The method according to claim 43, wherein the DNA molecule encodes a nitric oxide synthase comprising a protein or polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, and SEQ ID NO:6.
 49. The method according to claim 43, wherein the DNA molecule encodes a nitric oxide synthase comprising a protein or polypeptide having an amino acid motif selected from the group consisting of the motif of SEQ ID NO:7, the motif of SEQ ID NO:8, the motif of SEQ ID NO:9, the motif of SEQ ID NO:10, the motif of SEQ ID NO:11, the motif of SEQ ID NO:12, the motif of SEQ ID NO:13, the motif of SEQ ID NO:14, the motif of SEQ ID NO:15, the motif of SEQ ID NO:16, the motif of SEQ ID NO:17, the motif of SEQ ID NO:18, the motif of SEQ ID NO:19, the motif of SEQ ID NO:20, the motif of SEQ ID NO:21, the motif of SEQ ID NO:22, the motif of SEQ ID NO:23, the motif of SEQ ID NO:24, the motif of SEQ ID NO:25, the motif of SEQ ID NO:26, the motif of SEQ ID NO:27, the motif of SEQ ID NO:28, the motif of SEQ ID NO:29, the motif of SEQ ID NO:30, the motif of SEQ ID NO:31, the motif of SEQ ID NO:32, the motif of SEQ ID NO:33, the motif of SEQ ID NO:34, the motif of SEQ ID NO:35, the motif of SEQ ID NO:36, the motif of SEQ ID NO:37, the motif of SEQ ID NO:38, the motif of SEQ ID NO:39, the motif of SEQ ID NO:40, the motif of SEQ ID NO:41, the motif of SEQ ID NO:42, the motif of SEQ ID NO:43, the motif of SEQ ID NO:44, the motif of SEQ ID NO:45, the motif of SEQ ID NO:46, and combinations thereof.
 50. The method according to claim 43, wherein the nucleic acid molecule encodes a nitric oxide synthase comprising a protein or polypeptide having an amino acid sequence of SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, or SEQ ID NO:50.
 51. The method according to claim 43, wherein the nitrogen group is a nitro group or a nitroso group.
 52. The method according to claim 43, wherein the reaction is a nitration reaction or a nitrosylation reaction.
 53. The method according to claim 43, wherein the nitrogen-modified compound is a secondary metabolite.
 54. The method according to claim 53, wherein the secondary metabolite is selected from the group consisting of an alkaloid, a terpenoid, an aliphatic organic acid, an aromatic organic acid, a heteroaromatic organic acid, a phenol, an irridoid, a steroid, a volatile oil, a resin, a balsam, a β-lactam, an aminoglycoside, a macrolide, a tetracycline, and a saponin.
 55. The method according to claim 43, wherein the nitrogen-modified compound is a polyketide.
 56. The method according to claim 43, wherein the nitrogen-modified compound is a peptide.
 57. The method according to claim 56, wherein the peptide is a non-ribosomal peptide.
 58. The method according to claim 43, wherein the nitrogen-modified compound is a phytotoxin.
 59. The method according to claim 58, wherein the phytotoxin is thaxtomin.
 60. The method according to claim 43, wherein the nitrogen-modified compound is an herbicide, an antibiotic, or an anticancer agent.
 61. The method according to claim 60, wherein the antibiotic is chloramphenicol.
 62. The method according to claim 60, wherein the anticancer agent is L-alanosine.
 63. The method according to claim 43, wherein the nitrogen-modified compound is a high-energy material selected from the group consisting of nitroglycerin, trinitrotoluene, pentaerythriotoltetranitrate, cyclotrimethylenetrinitramine, and ammonium nitrate fertilizer.
 64. The method according to claim 43, wherein the target moiety comprises an electron-rich aromatic group.
 65. The method according to claim 43, wherein the target moiety comprises a phenyl moiety.
 66. The method according to claim 43, wherein the target moiety comprises an indole moiety.
 67. The method according to claim 43, wherein the target moiety comprises a tryptophanyl moiety.
 68. The method according to claim 43, wherein the non-modified compound containing a target moiety is provided exogenously.
 69. The method according to claim 43, wherein the non-modified compound containing a target moiety is produced by the transgenic host cell.
 70. A method of recombinantly producing a nitric oxide synthase in a host cell, said method comprising: transforming a host cell with at least one nucleic acid molecule according to claim 1, said transforming being performed under conditions suitable for expression of the nitric oxide synthase; and isolating the nitric oxide synthase.
 71. The method according to claim 70, wherein the host cell is selected from the group consisting of a bacterial cell, a yeast cell, a fungal cell, an insect cell, a plant cell, and a mammalian cell.
 72. The method according to claim 71, wherein the bacterial cell is. Streptomyces, Bacillus, Escherichia, Brevibacterium, Microbacterium, Nocardia, or Rhodococcus.
 73. The method according to claim 71, wherein the yeast cell is Saccharomyces.
 74. The method according to claim 71, wherein the fungal cell is Aspergillus, Cephalosporium, or Penicillium. 